<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: Class Members</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.4.3</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
      <li><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
      <li><a href="inherits.html"><span>Class&#160;Hierarchy</span></a></li>
      <li class="current"><a href="functions.html"><span>Class&#160;Members</span></a></li>
    </ul>
  </div>
  <div id="navrow3" class="tabs2">
    <ul class="tablist">
      <li class="current"><a href="functions.html"><span>All</span></a></li>
      <li><a href="functions_func.html"><span>Functions</span></a></li>
      <li><a href="functions_vars.html"><span>Variables</span></a></li>
      <li><a href="functions_type.html"><span>Typedefs</span></a></li>
      <li><a href="functions_enum.html"><span>Enumerations</span></a></li>
      <li><a href="functions_eval.html"><span>Enumerator</span></a></li>
      <li><a href="functions_rela.html"><span>Related&#160;Functions</span></a></li>
    </ul>
  </div>
  <div id="navrow4" class="tabs3">
    <ul class="tablist">
      <li><a href="functions.html#index_a"><span>a</span></a></li>
      <li><a href="functions_0x62.html#index_b"><span>b</span></a></li>
      <li><a href="functions_0x63.html#index_c"><span>c</span></a></li>
      <li><a href="functions_0x64.html#index_d"><span>d</span></a></li>
      <li><a href="functions_0x65.html#index_e"><span>e</span></a></li>
      <li><a href="functions_0x66.html#index_f"><span>f</span></a></li>
      <li><a href="functions_0x67.html#index_g"><span>g</span></a></li>
      <li><a href="functions_0x69.html#index_i"><span>i</span></a></li>
      <li><a href="functions_0x6b.html#index_k"><span>k</span></a></li>
      <li><a href="functions_0x6c.html#index_l"><span>l</span></a></li>
      <li><a href="functions_0x6d.html#index_m"><span>m</span></a></li>
      <li><a href="functions_0x6e.html#index_n"><span>n</span></a></li>
      <li><a href="functions_0x6f.html#index_o"><span>o</span></a></li>
      <li><a href="functions_0x70.html#index_p"><span>p</span></a></li>
      <li><a href="functions_0x71.html#index_q"><span>q</span></a></li>
      <li><a href="functions_0x72.html#index_r"><span>r</span></a></li>
      <li class="current"><a href="functions_0x73.html#index_s"><span>s</span></a></li>
      <li><a href="functions_0x74.html#index_t"><span>t</span></a></li>
      <li><a href="functions_0x75.html#index_u"><span>u</span></a></li>
      <li><a href="functions_0x76.html#index_v"><span>v</span></a></li>
      <li><a href="functions_0x77.html#index_w"><span>w</span></a></li>
      <li><a href="functions_0x78.html#index_x"><span>x</span></a></li>
      <li><a href="functions_0x79.html#index_y"><span>y</span></a></li>
      <li><a href="functions_0x7a.html#index_z"><span>z</span></a></li>
      <li><a href="functions_0x7e.html#index_0x7e"><span>~</span></a></li>
    </ul>
  </div>
</div>
<div class="contents">
<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>

<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
<li>score
: <a class="el" href="structmoltk_1_1dp_1_1RunningScore.html#a5814258bbf4fee728de4eb83486b32ed">moltk::dp::RunningScore&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__UNGAPPED__SEQUENCES_00_011_01_4.html#a4f927e74dfc33e81d635b08e074d7582">moltk::dp::RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_UNGAPPED_SEQUENCES, 1 &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1AlignmentResult.html#a8a554558c4efa955f56e4855be1e8136">moltk::dp::AlignmentResult&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a4eb58b41b9fef4021dd842b463d5d479">moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#acd68283be0040d5183e50ebd224d6600">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__GAPPED__ALIGNMENTS_00_011_01_4.html#a44d662dc9b3b6a78e987fae51442f20a">moltk::dp::RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_GAPPED_ALIGNMENTS, 1 &gt;</a>
, <a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#a28c8711e96b0ee8696f6e7436360a90d">moltk::dp::DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a>
, <a class="el" href="classmoltk_1_1MatrixScorer__.html#ab90650541e6f63c72b6a20a1480b2de7">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>scorer
: <a class="el" href="classmoltk_1_1Aligner.html#ae5864cedf09cec9ea5e8ea5967f505c9">moltk::Aligner</a>
</li>
<li>ScoreType
: <a class="el" href="structmoltk_1_1dp_1_1DPCell.html#ac40c80edc23e440bd171baa037a06448">moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>sequence_index
: <a class="el" href="classmoltk_1_1EString_1_1const__iterator.html#aebfe683ee618731fb3548e2f6a6d16f4">moltk::EString::const_iterator</a>
</li>
<li>sequence_weight
: <a class="el" href="classmoltk_1_1Alignment___1_1Row.html#a655f1804f8dd752f58c3c8c9ba0349c0">moltk::Alignment_&lt; SCORE_TYPE &gt;::Row</a>
</li>
<li>sequences
: <a class="el" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>set_default_gap_extension_score()
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#ae7fdb188444d50d14267783fd3bcba88">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>set_default_gap_open_score()
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#a6dce77af635e8e89b12eb632f88371f2">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>set_end_gaps_free()
: <a class="el" href="classmoltk_1_1MatrixScorer__.html#abe3caf1c15a2e325c7bd942b38fa8295">moltk::MatrixScorer_&lt; SCORE_TYPE, GAP_NSEGS &gt;</a>
</li>
<li>set_from_angle_about_unit_vector()
: <a class="el" href="classmoltk_1_1Rotation3D.html#a93cd577dd17fa9cbf1ba341baeb64ca1">moltk::Rotation3D</a>
</li>
<li>set_from_angle_axis()
: <a class="el" href="classmoltk_1_1Quaternion.html#affaf96ecdb1879a5c74ad281d39417f2">moltk::Quaternion</a>
</li>
<li>set_from_elements()
: <a class="el" href="classmoltk_1_1Rotation3D.html#a533ee2bc725541f6dfbf8e8e9769dbc1">moltk::Rotation3D</a>
</li>
<li>set_from_quaternion()
: <a class="el" href="classmoltk_1_1Rotation3D.html#a7509d7abc00a0349c45992e2471bd562">moltk::Rotation3D</a>
</li>
<li>set_pretty_width()
: <a class="el" href="classmoltk_1_1Alignment__.html#a0a7ba36b2af5bc886e8bcbc4fbdb4400">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>set_score()
: <a class="el" href="classmoltk_1_1Alignment__.html#a42cec9b9709afe53383953f3f687d16c">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>set_scorer()
: <a class="el" href="classmoltk_1_1Aligner.html#afac71af10ee7a0436853ae03b38f02dc">moltk::Aligner</a>
</li>
<li>SIZE
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a3624a981da731d31bae9b31cedebddb1">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>size()
: <a class="el" href="classmoltk_1_1Quaternion.html#aeb9b1be7a1bc9b90140803422c06b05c">moltk::Quaternion</a>
, <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a09385778cece4012604101127eb1942b">moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</a>
, <a class="el" href="classmoltk_1_1BaseVector3D.html#ad92f8ef5c2fd9b3c8cb09fce7e1b521b">moltk::BaseVector3D&lt; ELT &gt;</a>
</li>
<li>size_type
: <a class="el" href="classmoltk_1_1BaseVector3D.html#a946754e9570f3cdedc30b08fc9c7ec25">moltk::BaseVector3D&lt; ELT &gt;</a>
, <a class="el" href="classmoltk_1_1Quaternion.html#adea988431eacf534b466b34bce0fda5d">moltk::Quaternion</a>
</li>
<li>SquareRootType
: <a class="el" href="structmoltk_1_1units_1_1Quantity.html#a819bd6379a7cf717890d92d448439bab">moltk::units::Quantity&lt; U, Y &gt;</a>
, <a class="el" href="structmoltk_1_1units_1_1Unit.html#aec3622514f1535f0ff7eef06d83c0de1">moltk::units::Unit&lt; D &gt;</a>
, <a class="el" href="structmoltk_1_1units_1_1Dimension.html#ad234223c7c2dae7fe9d9a7a4cb0ebb7c">moltk::units::Dimension&lt; M, L, T, Q, N, A, I &gt;</a>
</li>
<li>SquareType
: <a class="el" href="structmoltk_1_1units_1_1Quantity.html#ab8db4eeb0cf1adc544fec23c12c0c070">moltk::units::Quantity&lt; U, Y &gt;</a>
, <a class="el" href="structmoltk_1_1units_1_1Unit.html#a11d0f74ab1654292bf50a66aced07fa5">moltk::units::Unit&lt; D &gt;</a>
, <a class="el" href="structmoltk_1_1units_1_1Dimension.html#ac9819c45990ae40740d2a68f190bf9d5">moltk::units::Dimension&lt; M, L, T, Q, N, A, I &gt;</a>
</li>
<li>structures
: <a class="el" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>
</li>
<li>SubstitutionMatrix_()
: <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#ad203d839a955f6cf1e2346993a7f6da8">moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</a>
</li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Friends</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
